Systems Biology, Sandia National Laboratories, Livermore, CA, USA.
Biotechnology and Bioengineering, Sandia National Laboratories, Livermore, CA, USA.
Sci Rep. 2018 Feb 16;8(1):3159. doi: 10.1038/s41598-018-21484-w.
Emerging sequencing technologies are allowing us to characterize environmental, clinical and laboratory samples with increasing speed and detail, including real-time analysis and interpretation of data. One example of this is being able to rapidly and accurately detect a wide range of pathogenic organisms, both in the clinic and the field. Genomes can have radically different GC content however, such that accurate sequence analysis can be challenging depending upon the technology used. Here, we have characterized the performance of the Oxford MinION nanopore sequencer for detection and evaluation of organisms with a range of genomic nucleotide bias. We have diagnosed the quality of base-calling across individual reads and discovered that the position within the read affects base-calling and quality scores. Finally, we have evaluated the performance of the current state-of-the-art neural network-based MinION basecaller, characterizing its behavior with respect to systemic errors as well as context- and sequence-specific errors. Overall, we present a detailed characterization the capabilities of the MinION in terms of generating high-accuracy sequence data from genomes with a wide range of nucleotide content. This study provides a framework for designing the appropriate experiments that are the likely to lead to accurate and rapid field-forward diagnostics.
新兴的测序技术使我们能够以越来越快的速度和越来越详细的方式描述环境、临床和实验室样本，包括实时分析和解释数据。其中一个例子是能够快速准确地检测广泛的致病生物，无论是在临床还是在野外。然而，基因组的 GC 含量可能有很大的不同，因此，根据所使用的技术，准确的序列分析可能具有挑战性。在这里，我们描述了 Oxford MinION 纳米孔测序仪在检测和评估具有一系列基因组核苷酸偏倚的生物方面的性能。我们已经诊断了各个读段的碱基调用质量，并发现读段内的位置会影响碱基调用和质量分数。最后，我们评估了当前最先进的基于神经网络的 MinION 碱基调用器的性能，描述了它在系统误差以及上下文和序列特异性误差方面的表现。总的来说，我们详细描述了 MinION 从具有广泛核苷酸含量的基因组中生成高精度序列数据的能力。这项研究为设计可能导致准确和快速现场诊断的适当实验提供了一个框架。
